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cozygene / FEAST

Fast expectation maximization for microbial source tracking
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Error in sprintf("Error: there are %d sample ids in common ") : too few arguments #27

Open develynw opened 3 years ago

develynw commented 3 years ago

I have been using FEAST on a microbiome analysis, but recently have come across the following error despite previously successful runs: image

I went through my code and input files, but don't see anything outstanding (screenshots below). I am stumped. Does anyone have insight on what could be causing this error?

AkilaMuthalagu commented 2 years ago

HI Develynw

I am stuck with the same issue. Did you get any solution for your issue, if yes can you please let me know

liashenhav commented 2 years ago

Do the sample ids in the metadata match the row names in the count matrix? You are also welcome to share your data files (feature table and metadata) so I can have a look. My email is: liashenhav@gmail.com

Best, Liat

anniewest commented 2 years ago

Hello, I have also had the same problem and was wondering if there had been an solution? My SampleIDs in the metadata and rownames in the count table are identical. Thanks

704913307 commented 2 years ago

Hello, Which package does the "feast" function originate from? how to load this package? Thanks

celiadl commented 2 years ago

Hello! I am facing the same problem. Is there any solution for it?

liashenhav commented 2 years ago

Dear Celia,

This error means that the out table (denoted ‘C = out_test’ in the FEST function) and your metadata (‘metadata_test’) don’t have shared sample ids. Please check your files and re-run.

I hope this helps.

Best, Liat

gauguinP commented 2 years ago

I try it twice. Focusing on C= otus. image image image the former is true while the latter face the same error. But it doesn't obey the input format that shown in the website.

stenoell commented 1 year ago

For anyone else facing this issue, I discovered that the documentation on the Github page doesn't match the R FEAST function; notably, the R help docs state: "The rownames of both C and the metadata table are the unique sample ids," while the Github documentation shows the sample ids as the column names for the counts table and implies that the sample ids should be a separate column in the metadata table. Once I changed the counts table and metadata so that the rownames in both were the sample ids, it functioned correctly.